|
Status |
Public on Apr 26, 2024 |
Title |
ESC, Input |
Sample type |
SRA |
|
|
Source name |
embryonic stem cells
|
Organism |
Gallus gallus |
Characteristics |
cell type: embryonic stem cells antibody: none
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Cells were fixed with 1% formaldehyde for 5 min at 37°C. After quenching and cell lysis, chromatin was sonicated using a Bioruptor (Diagenode). Libraries were prepared from immunoprecipitated DNA using the NEBNext® UltraTM Library Prep Kit by Helixo (https://www.helixio.fr/)
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Basecalls were performed using bcl2fastq 2.0. Quality control was performed on fastq files using the FastQC v0.11.3 software. Reads were aligned using Bowtie2 and multi-mapping reads were filtered out. Reads were aligned using Bowtie2 and multi-mapping reads were filtered out. SICER was used to identify the enriched regions in the immuno-precipitated samples compared to the input samples taken as control condition; MACS2 was used to confirm the outputs. Assembly: Gallus_gallus-5.0 Supplementary files format and content: List of the genome coordinates of the validated H3K9me3 domains for each cell type (csv format)
|
|
|
Submission date |
Nov 28, 2023 |
Last update date |
Apr 26, 2024 |
Contact name |
Clémence Kress |
E-mail(s) |
clemence.kress@inserm.fr
|
Organization name |
INRAE, Inserm
|
Lab |
U1208
|
Street address |
18 avenue du Doyen Lépine
|
City |
Bron |
ZIP/Postal code |
69500 |
Country |
France |
|
|
Platform ID |
GPL19787 |
Series (2) |
GSE248766 |
Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control [ChIP-Seq] |
GSE248768 |
Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control |
|
Relations |
BioSample |
SAMN38466829 |
SRA |
SRX22659364 |